BioC 3.6: CHECK report for SELEX on veracruz1

Package: SELEX

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SELEX_1.9.0.tar.gz

StartedAt: 2017-08-16 08:21:29 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:23:23 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 114.0 seconds

RetCode: 0

Status:  OK

CheckDir: SELEX.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SELEX_1.9.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SELEX.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SELEX/DESCRIPTION’ ... OK
* this is package ‘SELEX’ version ‘1.9.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SELEX’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
selex.config: no visible global function definition for ‘read.table’
selex.config: no visible global function definition for ‘write.table’
selex.counts: no visible global function definition for ‘flush.console’
selex.infogain: no visible global function definition for
  ‘flush.console’
selex.kmax: no visible global function definition for ‘flush.console’
selex.loadCountTable: no visible global function definition for
  ‘flush.console’
selex.mm: no visible global function definition for ‘flush.console’
selex.revcomp: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  complete.cases flush.console read.table write.table
Consider adding
  importFrom("stats", "complete.cases")
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
SELEX           25.503  3.354  12.396
selex.seqfilter  8.248  0.756   3.742
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/SELEX.Rcheck/00check.log’
for details.

* installing *source* package ‘SELEX’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SELEX)

name	user	system	elapsed
SELEX	25.503	3.354	12.396
selex.affinities	1.020	0.235	0.936
selex.config	0.215	0.059	0.157
selex.countSummary	1.170	0.248	0.894
selex.counts	1.628	0.275	1.080
selex.defineSample	0.257	0.063	0.156
selex.exampledata	0.186	0.062	0.147
selex.fastqPSFM	0.699	0.093	0.520
selex.getAttributes	0.259	0.079	0.238
selex.getRound0	0.285	0.081	0.278
selex.getSeqfilter	0.176	0.058	0.142
selex.infogain	1.985	0.550	1.604
selex.infogainSummary	0.908	0.221	0.689
selex.jvmStatus	0.238	0.058	0.166
selex.kmax	1.299	0.504	1.245
selex.kmerPSFM	0.495	0.140	0.438
selex.loadAnnotation	0.461	0.081	0.266
selex.mm	1.025	0.203	0.645
selex.mmProb	0.456	0.187	0.580
selex.mmSummary	0.675	0.205	0.670
selex.revcomp	0.805	0.212	0.985
selex.run	2.320	0.495	1.509
selex.sample	0.294	0.079	0.245
selex.samplePSFM	0.472	0.081	0.378
selex.sampleSummary	0.184	0.078	0.226
selex.saveAnnotation	0.096	0.066	0.151
selex.seqfilter	8.248	0.756	3.742
selex.setwd	0.078	0.048	0.112
selex.split	0.474	0.164	0.492
selex.summary	1.302	0.466	1.439